microarrays for mapping and expression analysis: toward the genetic determinants of light response...
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Microarrays for mapping and expression analysis: Toward the genetic determinants of light response adaptation in Arabidopsis and Aquilegia
Justin BorevitzEcology & EvolutionUniversity of Chicagonaturalvariation.org
Light Affects the Entire Plant Life Cycle
Light response variation can be seen under constant conditions in the lab
Seasons in the Growth Chamber
• Changing Day length• Cycle Light Intensity• Cycle Light Colors• Cycle Temperature
Sweden Spain
Seasons in the Growth Chamber
• Changing Day length
• Cycle Light Intensity
• Cycle Light Colors
• Cycle Temperature
Day Length
0:00
2:00
4:00
6:00
8:00
10:00
12:00
14:00
16:00
18:00
20:00
22:00
sep
oct
nov
dec
jan
feb
mar
apr
may jun jul
aug
month
hour
s
Sweden
Spain
standard
standard
Light Intensity
0
200
400
600
800
1000
1200
1400se
p
oct
nov
dec
jan
feb
mar
apr
may jun jul
aug
month
W/m
2
Sweden
Spain
standard
Temperature
-10
-5
0
5
10
15
20
25
30
35
sep
oct
nov
dec
jan
feb
mar
apr
may jun jul
aug
monthde
gree
s C
Spain High
Spain Low
Sweden High
Sweden Low
standard
Talk Outline
• Single Feature Polymorphisms (SFPs)– Potential deletions
– Bulk segregant/ eXtreme Mapping
• Haplotype analysis
• Tiling arrays
• Aquilegia
• Single Feature Polymorphisms (SFPs)– Potential deletions
– Bulk segregant/ eXtreme Mapping
• Haplotype analysis
• Tiling arrays
• Aquilegia
What is Array Genotyping?
• Affymetrix tiling array GeneChips contain ~35bp spacing, 1.67million unique features
• Genomic DNA is randomly labeled
with biotin dCTP, product ~50bp.
• 3 independent biological replicates compared to the reference strain Col
GeneChip
False Discovery and Sensitivity
PM only
SAM threshold
5% FDR
GeneChip SFPs nonSFPs Cereon marker accuracy 3806 89118 100% Sequence 817 121 696 Sensitivity
Polymorphic 340 117 223 34% Non-polymorphic 477 4 473
False Discovery rate: 3% Test for independence of all factors: Chisq = 177.34, df = 1, p-value = 1.845e-40 SAM threshold 18% FDR
GeneChip SFPs nonSFPs Cereon marker accuracy 10627 82297 100% Sequence 817 223 594 Sensitivity
Polymorphic 340 195 145 57% Non-polymorphic 477 28 449
False Discovery rate: 13% Test for independence of all factors: Chisq = 265.13, df = 1, p-value = 1.309e-59
3/4 Cvi markers were also confirmed in PHYB
90% 80% 70%
41% 53% 85%
90% 80% 70%
67% 85% 100%
Cereonmay be asequencingError
TIGRmatch isa match
Chip genotyping of a Recombinant Inbred Line
29kb interval
Discovery 6 replicates X $500 120,000 SFPs = $0.025Typing 1 replicate X $500 120,000 SFPs = $0.0041
Potential Deletions
>500 potential deletions45 confirmed by Ler sequence
23 (of 114) transposons
Disease Resistance(R) gene clusters
Single R gene deletions
Genes involved in Secondary metabolism
Unknown genes
Potential Deletions Suggest Candidate Genes
FLOWERING1 QTL
Chr1 (bp)
Flowering Time QTL caused by a natural deletion in FLM (Werner et al, Genetics 2005)
MAF1
FLM natural deletion
Fast Neutron deletions
FKF1 80kb deletion CHR1 cry2 10kb deletion CHR1
HetHazen et al Plant Physiology 2005
LUX ARRHYTHMO encodes a Myb domain
protein essential for circadian rhythms
Hazen et al PNAS, 2005
Cloned with Array Mapping
LOD
eXtreme Array Mapping
Allele frequencies determined by SFP genotyping. Thresholds set by simulations
0
4
8
12
16
0 20 40 60 80 100cM
LO
D
Composite Interval Mapping
RED2 QTL
Chromosome 2
RED2 QTL 12cM
Red light QTL RED2 from 100 Kas/ Col RILs
Array Haplotyping
• What about Diversity/selection across the genome?
• A genome wide estimate of population genetics parameters, θw, π, Tajima’D, ρ
• LD decay, Haplotype block size• Deep population structure?• Col, Lz, Bur, Ler, Bay, Shah, Cvi, Kas,
C24, Est, Kin, Mt, Nd, Sorbo, Van, Ws2Fl-1, Ita-0, Mr-0, St-0, Sah-0
Array Haplotyping
Inbred lines
Low effectiverecombinationdue to partialselfing
Extensive LDblocks
Col Ler Cvi Kas Bay Shah Lz Nd
Chr
omos
ome1
~50
0kb
Review
• Single Feature Polymorphisms (SFPs) can be used to
• Potential deletions (candidate genes)• Identify recombination breakpoints• eXtreme Array Mapping
• Haplotyping• Diversity/Selection
• Association Mapping
RNA DNA
Universal Whole Genome Array
Transcriptome AtlasExpression levelsTissues specificity
Transcriptome AtlasExpression levelsTissues specificity
Gene DiscoveryGene model correctionNon-coding/ micro-RNAAntisense transcription
Gene DiscoveryGene model correctionNon-coding/ micro-RNAAntisense transcription
Alternative SplicingAlternative Splicing Comparative GenomeHybridization (CGH)
Insertion/Deletions
Comparative GenomeHybridization (CGH)
Insertion/Deletions
MethylationMethylation
ChromatinImmunoprecipitation
ChIP chip
ChromatinImmunoprecipitation
ChIP chip
Polymorphism SFPsDiscovery/Genotyping
Polymorphism SFPsDiscovery/Genotyping
~35 bp tile, non-repetitive regions, “good” binding oligos, evenly spaced
SNP SFP MMMMM MSFP
SFP
MMMMM M
Chromosome (bp)
con
serv
atio
n
SNP
ORFa
start AAAAA
Tra
nsc
ripto
me
Atla
s
ORFb
deletion
Improved Genome Annotation
• 300 F3 RILs growing (Evadne Smith)• >50,000 ESTs TIGR gene index and GenBank,
arrays being designed by Nimblegen
Aquilegia (Columbines)
NSF Genome Complexity
• 52,000 ESTs 5’ and 3’– >9k contigs, 4k singletons
– >500 SNPs
• 350 arrays, RNA and genotyping– High density SFP Genetic Map
• Physical Map (BAC tiling path)– Physical assignment of ESTs
• QTL for pollinator preference – ~400 RILs, map abiotic stress
– QTL fine mapping/ LD mapping
• Develop transformation techniques
• http://www.AQgenome.org
Scott Hodges (UCSB)
Elena Kramer (Harvard)
Magnus Nordborg (USC)
Justin Borevitz (U Chicago)
Jeff Tompkins (Clemson)
University of Chicago
Xu ZhangEvadne Smith
University of Guelph, Canada
Dave Wolyn
Sainsbury Laboratory
Jonathan Jones
NaturalVariation.orgNaturalVariation.orgSalk
Jon WernerJoanne ChoryDetlef WeigelJoseph Ecker
UC Davis
Julin Maloof
UC San Diego
Charles Berry
Scripps
Sam HazenElizabeth Winzeler
Salk
Jon WernerJoanne ChoryDetlef WeigelJoseph Ecker
UC Davis
Julin Maloof
UC San Diego
Charles Berry
Scripps
Sam HazenElizabeth Winzeler
University of Chicago
Xu ZhangEvadne Smith
University of Guelph, Canada
Dave Wolyn
Sainsbury Laboratory
Jonathan Jones